The Phantom Theory
by Shadic999
Summary: A new breed of ghost has started to take over both the real and ghost worlds, and Danny stands it the middle of the conflict. But when he is faced with choices that could decide the fate of himself and his friends, will he choose correctly? In a deep, twisting plot, Danny will discover the price of being the superhero everyone needshimtobe. Rated M for violence and eventual lemons.
1. Prologue and The Big Day

Hello everyone! It is Shadic999! Now, chances are that no one has actually missed me in the almost two years that it has been since I have done any serious writing, but that is hopefully going to change now. I have been spending the time in school and we all know how such trivialities can make us lose sight of what is important XD. Anyway, I was struck by inspiration after having read a fairly poor fanfic, and decided that it was about time I gave the world another reason to believe that I'm a crazy pervert. But in all honesty, this is a first attempt at writing a long story in just as long of a time, so I need good advice in order to get back in the swing of things. I will always ramble like this at the beginning of chapters, but I'm sure you will find it nonetheless entertaining. Also, as I think it's only fair, the people who help the most may have a say in how this story plays out. I'll shut up now. Enjoy!

Prologue

Danny Fenton was sitting alone, on a hilltop far from Amity Park. The warm summer breeze, accompanied by the red hues of the setting sun caused an almost palpable aura of peace. It was in this place that Danny was truly able to find an escape. This place, this sanctuary, was where he retreated to in order to escape from the frantic life of Danny Phantom. He did not regret the path his life had taken, gaining ghost powers, saving the world, and still balancing it with his teenage life with his friends, but he needed these short respites. He watched as the sun set that evening, his life simple in his mind. He was going to graduate from Casper High tomorrow, somehow with honors, and he was beginning to envision the life he wanted with his friends. He glanced down at his phone, noticing that he had missed a text from his mother asking for him to come home. He sighed and Morphed, his regular clothes disappearing, being replaced with the iconic black and silver suit that Danny Phantom was famous for.

It was a short flight home from the hilltop, and as Danny arrived home, he Morphed again and resumed his form as Danny Fenton. He tried to sneak in the door but was instead greeted by his mother, Maddie.

"Where were you Danny? You had me worried. I tried calling Sam and Tucker, but neither of them knew where you were."

"Mom, really, I was just taking a walk. Nothing to get all riled up about."

"Well fine, but the family has already eaten. You'll have to fix something for yourself."

Danny grumbled and walked into the kitchen and made some instant noodles. He then clambered up the stairs to his room. He sighed for a moment lost in thought. That night was quiet, the world was peaceful, and that was the last night like that for Danny for a long time.

Chapter 1- The Big Day

"Danny! Get your lazy ass out of bed!" screamed Jazz, "You're going to be late!" Danny shot straight up in his bed, eyes wide. "AAAHHH! I'm late!" Racing out of bed, he grabbed his dressy black shirt and pants along with his new silver tie. He threw on the clothes, and brushed his teeth, almost gagging on the toothbrush in the process. He ran down the steps, nearly running over his parents. They were hardly perturbed. "Aww, Danny, you are so grown up," Maddie said with a smile, taking hold of Jack's hand. Jack put his free hand on Danny's shoulder, "Son, you have made me so proud. Someday you may even be able to invent new ghost tech with your father!"

"Oh now Jack," said Maddie, "Today is about Danny. Let's not spoil it.

"I still don't see how talking about ghosts could possibly be a bad thing…"

"Jack…" she said sternly.

"Alright."

"Hey, um, guys, loving the chit chat, but I really need to go," said Danny.

"Ok Danny, well see you at the ceremony," replied his mother.

Danny got out of the house, quickly Morphed, and flew to school. Far below, a pair of unseen eyes followed his form, streaking across the sky. "Have you confirmed his location?" asked a voice, crackling over the radio that the unseen figure held.

"Yes I have. I believe that the subject is heading to the high school. Please advise."

"Follow him. We must make sure that this goes according to plan."

The figure rose, standing at just over 6'. He turned invisible and followed in the air, making sure not to be detected.

When Danny arrived at the school, he found a good place to Morph and quickly found his best friends, Sam and Tucker, standing near the entrance to the stage where the graduation was to take place. "Dude, where were you? The whole thing is about to begin!"

"Tucker is right Danny, you were cutting it close today."

"Guys, look, I made it on time. Besides, this is GRADUATION. Let's just have fun today alright?" pleaded Danny.

"Ok, fine, but Danny, it is important," said Sam. "Today is really important. I just don't want anything to go wrong."

"Sheesh Sam," said Tucker, "why such a worry wart all of a sudden. You don't even get this worked up when we go ghost hunting."

"Because I know that Danny knows what he's doing fighting ghosts. He can just be so stupid like this."

"Ok Sam, I screwed up. Big deal. Can we just go in now?"

The graduation went well enough. The whole thing ran smoothly, with only the occasional stutter by one of the stagefrightened students who had to give speeches. Tucker fell asleep at one point, but a quick jab to the ribs was enough to rouse him. At last their names were called. The three friends stood together on stage, beaming at the flashing cameras and cheering audience.

That afternoon, as the day wound down, the three found themselves hopping from party to party, talking to people and just having a good time. At Paulina's house, half of the guests were getting slammed while the other half were getting high or laid. It was in that decadent slumhole that Danny's ghost sense went off. He turned his head and locked eyes with a figure covered in a dark robe that concealed the wearer's face. The hooded figure approached Danny, spoke in a deep, feminine voice, "Danny, you aren't safe here. You need to leave now." It was Ember of all ghosts.

"Ember, what are you doing here? What's going on?"

"I could ask you the same question, dipstick, but we don't have time for this. You need to leave now. Something terrible is about to happen, and you won't be able to stop it."

"Ember, what do you mean? You aren't making any sense. What is going to happen?"

"Danny, there is no time. Leave NOW!"

In the split second that followed, an explosion shook the room, completely demolishing the southern wall, and causing large portions of the ceiling to fall. Ember turned the two of them intangible and they made it through the event unscathed. But the same could not be said for many of the other partygoers. Several of them had suffered severe injuries. Many had broken bones and were bleeding profusely from the gashes left by the shrapnel. Danny looked around in disbelief, shocked by the sudden violence.

He could feel a pressure under his arms, raising him into the air. It was Ember, flying him away from the destruction. He didn't even care. His only thoughts were of the people who were caught in the blast; the shapes and odd contortions that the bodies were in, splayed in horrible angles. But just then, a horrible thought forced itself into his mind. One thought so potent that he was forced out of the numbness. "SAM! TUCKER!" He immediately Morphed and struggled to escape from her grip. "Please forgive me Danny," said Ember, and Danny felt a pinch in his shoulder as a needle was forced in, the potent drugs immediately taking hold on his mind. His vision started to turn black and he could feel the numbing effects of the drug immediately putting him to sleep.

He was sure he was dreaming. The muffled sounds and shapes that moved around him seemed so strange, so foreign to his senses. Everything was grey, and he was having a hard time making out one shape from another. He almost thought that he could make out Ember's form. Images flashed before his eyes; a castle in the distance, long stone hallways, stairwells that went downward forever, and finally a sterile white room that seemed so out of place to him. He awoke to a start, an IV running into his arm, a clear yellow-green fluid flowing into his arm. He felt lethargic, and his limbs felt heavy. It took an immense amount of willpower in order to get himself into a sitting position. That's when a door from behind slid open and the voice of Vlad Masters filled the room. "Wake up little badger, you are needed.

A/N: And that was chapter one! What do you think? I want lots of reviews! And a personal shoutout to a good friend of mine in California; without your support, this story would probably never have come about. The next chapters will probably be longer, but don't expect stories to be on a set schedule. Just follow me and check your email. They won't be far apart, but the more likes, comments, etc., will make chapters come out a lot faster. So thanks for reading. And to all my adoring fans, (the few of you that are out there) I promise not to disappoint ;)


	2. A Brief Awakening

So while I'm writing this, I haven't actually had any hits on the first chapter yet, but I remain ever vigilant in my hopes that one of you will leave me a comment/review. Anyways, in unrelated news, I have decided to start typing this on my phone because it is so much more convenient than trying to hold my laptop over my face while in bed. Not only that, but it hurts a heck of a lot less when I drop it on said face. Yes, it happened. Don't ask me how. All you need to know is that the next chapter is up :)

Chapter 2 -

"Calm down Daniel, you struggling is not going to help anything!" Exclaimed Vlad as he was trying to hold Danny down on the table.

"Let me go! What are you doing to me?"

"Daniel!" Vlad shouted, stunning Danny for long enough to speak. "An ectobomb was detonated at the party you were at. You suffered from a concussion and two broken ribs. You would have died had Ember not protected you, and despite that you were still wounded.

Danny could feel the twinge of pain that raced through his chest when Clad mentioned the ribs, and even be had to admit that be was finding it hard to focus his eyes. "There's nothing to be afraid of now, your high ghost energy will speed the healing process."

"How is Ember? Is she alright?" asked Danny.

"Yes, she will be fine. She took more shrapnel due to her protecting you, but she is expected to make a full recovery." Then Vlad added jokingly, "It's hard to kill a ghost, Daniel. You should know that well enough by now."

Danny huffed at that, sending a slight twinge through his body. "I suppose so. Where is she?"

"In a recovery room down the hall. You will be allowed to see her later, but right now we have some extremely important matters to attend to. Can you walk?"

Danny stirred, and righted himself in his bed. Than he stood, a little wobbly at first, but soon steadied and found he could in fact stand. "How long was I out?" asked Danny.

"8 hours after Ember administered the drug. You were struggling against her and in her condition, she couldn't risk you getting away from her."

There was a feeling in the back of Danny's mind, some lost thought struggling to surface. It hit him. "Sam and Tucker. What happened to them?" Vlad's face darkened and be let out a sigh. "I'm sorry Daniel" we weren't able to recover the bodies. We can only assume that they were killed in the blast. I'm so sorry Daniel. We did all that we could."

Danny's throat turned dry and he began to sweat. The color drained from his features, his breathing sped up, and a look of confusion took over his features. "What are you saying?"

"Daniel, you're friends are most likely dead."

Danny realized that he was screaming. Everything was a blur as be fired a ghost ray at Vlad in the chest. He Morphed and became intangible, taking a deep breath, he flew through the wall and then straight up. He came up through the ground and rocketed upwards and unleashed his Ghostly Wail; the screeching sonic blast shattered the morning calm. He poured his anger and pain into the blast and as he drained himself of power, he began to revert to his human form, shreds of his ghostly form being torn from him as the Wail continued. Eventually, he had nothing left to give it, and he fell from the sky, hitting branches on his way down, and crashing violently into the ground. He wept. He screamed in sheer agony, not even feeling the newly broken collarbone. He couldn't control himself. Vlad, in his ghost form floated towards him, scooped the crying child up in his arms, and flew him back to the castle. Behind him was a smoking quarter mile of the smoking remains of the Wisconsin landscape.

And that's chapter two! Did anyone expect that? My killing off Sam and Tucker? Or that Vlad isn't actually behind the attack? Anything? Now, I know this chapter is short, but I have a reason. I plan on dividing chapters by events and perhaps POVs, but I haven't really decided if I want to break from the third person. If I get enough support for something like that though, you will definitely see dome first person action. Also, I know this chapter was short guys, I get that. And I am sorry. Again, I want to keep story elements separate if at all possible (for now) Next on the agenda, I am thinking about revisiting my old smuts and editing them a bit to make them sound less like a 13/14 year old wrote them, and more like a 16 year old wrote them XD. Let's see, anything else…? Oh yeah! How could I forget!? I got my first review today :D Shoutout to RASKOV. Thank you so much for the comment! I know it seems stupid, but to see such an immediate response was almost overwhelming. I appreciate it a lot :D And guys, I still need advice, I know its not much to work with yet, but I need it for this story to go well. So thank you for reading and yeah. Anticlimactic ending for the win! XD


	3. Chapter 3 - The Training Begins

Ok, so I keep asking myself, "Does one actually write whole chapters in one sitting?" Because I've been finding it difficult to just sit down and type. Anyway, I'm on an airplane flying from Houston back to my house (the whereabouts of which shall remain a mystery MWAHAHAHA) The point is, I'm using my smartphone, so I apologize if there are some typos, etc. I'm trying my best to proofread, but I'm not even reading this. For some reason, the gloom of a storm outside my port side window is far more intriguing to me that my inability to type. Je ne sais pas pourquoi... As always, a little shout out to my few fans who are actually reading this and care that I'm basically rambling. Umm... Side note, for the people who are interested in really helping me out, I'd appreciate a PM. This means that only semi-experienced writers will have a lot to say, and them everyone else can get accounts and tell me what to do, or just leave praise in the comments for the story so more fools, people I mean, read this. So thank you for your cooperation :) Enjoy!

Chapter 3 - The Training Begins

Danny was woken by Ember at precisely 6 o' clock in the morning, as per Vlad's Instruction. "Danny, get your lazy ass out of bed!" He rolled his eyes at her and rolled over. Ember responded, rather patiently, by smashing her guitar into him, sending his body sprawling on the floor.

"The heck was that for?" shouted Danny.

"Because you weren't waking up. Vlad wants us to be downstairs for briefing this morning."

"Briefing? What do you mean?" asked Danny, turning suddenly serious.

"All I know is that Vlad has something big that he has been waiting to tell us. I I know a bit about it already, but he has been sending spies to learn more."

"Spies? What for? Why haven't I been told anything?"

"He will be explaining things downstairs. Be there in ten minutes." Then Ember phased out of the room, leaving Danny alone to his thoughts. His head was spinning. Why would Vlad need spies? He was always one to go for things head-on. Even when stealing the Crown of Fire and the Ring of Rage, he had been undaunted by the danger. Vlad could be very heavy-handed at times... So what could be so unsettling that he felt he should use spies? It was this curiosity and lingering adrenaline that fueled him to get dressed in the form-fitting black gear that was left by Ember, and he followed suit, Morphing and phased out of the room.

...

In an underground laboratory, two figures were sitting in high backed chairs, peering over several monitors that were attached to a computer that dominated one of the walls in what would be considered a small room. There were some sparse furnishings here, a desk, some bookshelves filled with various documents, but he room was completely white, and incredibly sterile, even by scientific standards. The scientists murmured to each other, day after day, their work progressing slowly, but surely. One of the two gasped suddenly, shock lining his face. It was impossible he thought, but after all, this was his life's work. Perhaps he had finally found the key... He ran over to his shelves, and pulled out several documents, making quick notes on the pages and comparing them to his readings. He was sure of it. He could do the impossible now. He just needed one more ingredient...

...

Danny was sitting in a small semicircle, with Valerie and Ember, and they were waiting for Vlad to speak. He took in a deep breath and began. "Danny, first you should know that Valerie knows about your alter ego. Now is not the time to discuss it, however." Danny was bewildered, but it had confirmed his fears, this was serious. "I know that you three are most likely very confused as to why you are here. Something is happening in the ghost zone. Something altogether different from anything we have ever seen before. Even Pariah Dark was nothing compared to this new threat. I have been recently been informed that the Guys in White have been developing a new procedure that is supposed to be a drastic new step in fighting ghosts. From what I have gathered, they have been somehow modifying humans to be more capable of fighting ghosts. But these subjects have been experiencing side effects, things like violent outbreaks, hallucinations, paranoia, and acute psychopathy. Coupled with enhanced strength and agility, these are a serious threat to ghosts. Now normally, I would not bother you three with this kind of information. The GiW has been trying to do something like this for years. But they have never been this successful. Knowing that he GiW has always wanted to see an eradication of all ghosts, I am becoming more and more concerned with their activities. So I plan on not only informing you three of whatever I can, but I want to train you, to be able to counter this threat, and eventually be able to investigate this issue further. I will be pairing you each with a partner. You will watch each other's back at all times. I fear for your safety. Therefore, Daniel, Ember, you are partners. Valerie, you will be with me until a more suitable partner presents themselves. I am however looking into it. Your training will begin today at 8. Meet in the field outside. That is all." He then walked out, leaving them speechless.

It was Valerie who spoke first. "What kind of modifying does he mean? I know there are things like steroids and meds, even I had some when I started ghost hunting. But they were mostly ineffective, and I never had anything worse than nausea."

Ember nodded at that. And Danny had to agree, a new drug seemed to make sense. But there was a persistent nagging at the back of his mind. Something wasn't right. He stood up then, "Let's head out." I want to see what kind of training he has in mind.

...

It was a beautiful day outside, the sun was just beginning to show above the far off hills. There were signs of animal activity, birds chirping and squirrels chattering away, enjoying the brisk morning air. This was the first time that Danny could really take a look at his new gear. The clothes were a thin black fabric that were ever so slightly loose in his body, but by no means was bulky. There were hardened plates over his forearms, shoulders, chest, and the entire design was simple. Spartan almost. The color of it was odd though. It wasn't black as be had originally assumed, but a darkly mottled green and grey, that blended well into the shadows of the forest. He was joined by Valerie and Ember, who were wearing similar gear.

Vlad suddenly appeared, carrying a duffel bag. "Today will be focused on ascertaining where you are physically, so we know what needs to be improved the most. Danny, we have fought several times in the past, but today will be a formal assessment of your abilities. Ember, as I understand, you posess an immense amount of strength for your age, but lack the agility to properly wield it. And finally Valerie, you have been mor or less dependent of your gear to assist you in battle. We must wean you off of those boons, and start training you unarmed. We will be assessing strength as well as speed in various conditions." He pointed to the front doors of the estate and spoke to them. "On foot the three of you are to run, not fly, retrieve a baton from the porch. The run will be about a mile, and you will be timed. Go."

Danny was dashed off, but he had obviously misjudged how fit he was in his human form. He was well ahead of the other two though, and felt confident that he would beat the two of them back. Ember was struggling in her own way, being a ghost had allowed her to become dependent on her ability to fly effortlessly. She had to teach herself the coordination to be able to walk well, let alone run. Valerie was struggling as well. She wasn't used to not having oxygen supplied to her, and despite her best efforts, she was unable to maintain the pace she had wanted to. Danny did in fact finish first, but was disappointed with an 8 minute mile. Ember and Valerie followed not to far behind. Vlad was disappointed, and clicked his teeth seeing how slow hey had been. The assessment continued, including several exercises and leaving the trio deflated at the end of the day.

That evening Vlad had told them that they had a ways to go, but believed that wih effort, they would soon be far more physically capable. They enjoyed a meal that Vlad had prepared by a servant in the house, and the day ended with a sense of disappointment.

The next morning was much like the last, with everyone assembled outside. Vlad this time was wearing his own suit of dark armor. "Today, we will be discussing some of the weapons that you will be using. For those of you with ghost powers, you will eventually be taught to synthesize many of these weapons, but Valerie, you will need to take especial care of your weapons." He drew out three swords, two of them a translucent metal, that almost was more of a mist than a blade. The third was a three foot blade that was made of a dark metal that shone dully in the morning light. The cthree inspected their weapons for a moment, and turned to Vlad who had sheaths for the weapons. He startled them to their backs and showed them how to sheathe their weapons. After that, he handed them each a double scabbard that held two heavy knives made of the same black material as Valerie's sword. "These weapons, and your armor in fact, is made of an extremely strong material that is produced by smelting steel with ghost energy. The outcome is an extremely strong alloy that is resistant to direct blasts of ghost energy, but otherwise has the same properties as steel. It is completely phasable, so tangibility and invisibility can still be achieved." As for the swords, you will be sent to a trainer of my choosing when the time comes. The same will apply to knife training. Daniel, Ember, draw your swords." They did so. Now I want you to focus your ghost energy into the blade, as if you were charging a ghost ray." Again, they did so, and the mist that made up the blade glowed and a thin, glowing blade sprang from the hilt. It was a glimmering blue and silver color and Danny could tell that it was razor sharp. "Woah!" Said Ember, surprised in the blade's sudden appearance. Vlad turned to them. "Eventually you will be able to create these blades and several other objects without the special hilts that I have provided for you. That will be included in your training." Turning to Valerie, he said, "Obviously you will not be able to produce these blades, so I have provided you with a Darkmetal blade." Including the rat of the group, he continued, "You will be expected to learn to wield these weapons. We will begin that training today, but you will need practice. Lots of it."

Hours later, the three were exhausted. Despite how light the blades were, their bodies ached from the exertion, but if you looked into their eyes, something had changed. They wore a look of determination now. That they were becoming something more.

Quick shout out to Jackie! She's turning 17 and I'd love it if you all wished her a happy birthday in the reviews! Let's make it special! Also, school is coming up, so I can't promise weekly updates, but I am going to try. Not sure if I'm going to keep the armors or not... Tell me what you think! -Shadic999


	4. Chapter 4 - Briefing

Alrighty, I'm not sure why I keep writing before I actually get any comments on my story... But here goes! XD

Chapter 4 - Briefing

Three months had gone by since the trio had begun their training. Within the first week Dani had joined their entourage and became Valerie's partner. The months had been good to the group. The four had become more or less proficient wielding their new weapons, and their progress was astonishing. Valerie had proven to be a natural with the blades, her extensive use of fairly modern technology had given her practice that have her an almost graceful efficiency with her knives. Ember, on the other hand, having such prowess with her ghostly power, had taken to the blade, using it the way she had wielded her guitar. Danny however was struggling, but he had one advantage over the others; he was lightening fast. His movements, though somewhat clumsy, were a blur to the casual onlooker, and Vlad, with years of practice found it hard to defend from the blade that could strike anywhere, seemingly at will.

Dani had not been given the same weapons however. Vlad had suspected that her talents lied elsewhere. He knew she was powerful and resourceful, but he had given her one on one training, teaching her to balance her powers, and to prevent her potential meltdowns; where her body began to disintegrate due to energy overexpendature, and instead taught her healing methods and special medicine. The four of them were now a real force to be reckoned with.

Their bodies had changed as well, Valerie and Ember had both slimmed considerably, their bodies showing their new athleticism. Danny had filled out, his muscles now showing, taught underneath his skin. It was no small point of pride to him that he now possessed a six pack, and he could now appreciate his look in the mirror. It had been hard work, and they could see the results.

Today had an odd air to it, they group could tell that something was different when they sat at the conference room that Vlad had been using for their lessons in ghost history, warfare, and espionage. There was a tension in the air, and the room felt a few degrees colder than it normally would. Then Vlad floated into the room, his face covered in some emotion that Danny could hardly make out. It was a look of confusion, anger, and something in his mind registered, disgust. Vlad took a deep breath and began talking to them. "Today you are to begin your first assignment. We have located one of the Guys in White experimental laboratories. We believe that they have one of their subjects that have been undergoing their mutagenic process stored there. Your mission will be to infiltrate their holding, and to collect samples of the building and whatever materials you can find. I want everything that you can get, pictures, security system details, floor layouts, etc., but your top priority will be in obtaining tissue samples from the test subjects. I hope to be able to analyze the blood and tissue samples you collect, to try and figure out what exactly they have been doing. Remember, these people are highly trained in detecting ghosts and intruders alike. I will supply you with the materials you will need to get inside, but then it will be up to you. Do not allow yourselves to be captured. If I see anything going wrong, I will tell you to abort the mission. Any questions?"

Danny looked at the others with a look of concern. Vlad hadn't asked them to do anything that they weren't trained to do, but they had always been supervised. This was going to be real, with real consequences for failing. "Alright," said Danny, his eyes turning back to Vlad, "What is the plan?"

"I'm glad you asked Daniel, as you will be leading this mission. You and Valerie are to go undercover as replacement chemists. I had two of the men bribed to not be at the labs that day."

"What about Ember and Dani? Where will they be?" Danny wouldn't admit it to himself, but he was growing rather fond of Ember, and realized with a start, that he wanted her to be at his side during this.

"Ember will overshadow you, and Dani will be overshadowing Valerie. I know you are most likely uncomfortable with the prospect, but they will passively overshadow you. In other words, you will retain control of your thoughts and bodies. It is the only way for two ghosts to get in."

Valerie interjected then, "But can't Dani become human by Morphing? Why can't we just take her in that way?"

"She is far too young to pass off as a scientist, and the fewer bodies we send in, the less likely you are to be discovered."

Valerie had no way to retort and she fell silent.

Dani spoke up, "Don't worry Val, I'm not looking forward to it too much either, but on the bright side, I can let you use my ghost powers in the mean time, so you may actually enjoy it," she remarked laughing now. Even the grim Valerie had to crack a smile at that.

Vlad cleared his voice again, and the room fell silent. "True. Daniel, you will find that your powers will be magnified as well, just keep in mind that whatever form of exhaustion you feel, Ember will as well, and avoid falling unconscious while Merged. There are stories of ghosts being unable to break apart after falling unconscious whiled Merged. I would hate to see that happen. The plan will go into effect tomorrow. For today, you have the day off. Use it as you will." He then left the room.

Dani jumped up at that. "Awesome! I'm totally going swimming in the lake. Come on Val!"

"Alright, kid. I'm coming," she said laughing enthusiastically.

A dark look came over Danny, and Ember thought she had just imagined it, but because of their partnering, she knew that something was wrong. He Morphed and slowly flew out of he room. Ember decided to follow him.

...

Danny landed in the Amity Park Cemetery. He was invisible, and he slowly walked through the gravestones until his eyes fell on three in particular, lined up neatly next to each other. The letters were clearly engraved into the stone, but the tears in Danny's eyes kept him from easily making out the words. The first gravestone read

"Here lies Tucker Foley,

Friend and true companion,

He will be remember as a loyal partner.

1996-2015"

The second,

"Here lies Samantha Manson,

Her unique way of changing lives will never be forgotten.

Her loyalty was unwavering, and she protected those she loved."

1996-2015.

And finally,

"Here lies Danny Fenton,

The prodigal son of the Fenton Family,

Though you are a time and a life away,

You will always be loved.

1996-2015"

Danny turned his gaze, crying softly, not bothering with the tears that streamed down his face. His quiet sobs going unheard. Ember landed behind him, and saw the boy's shoulders shaking, his pain evident, and she immediately realized to whom the graves belonged. She walked quietly to him, and wrapped her arms around him. Without thinking, Danny pulled her close to him, tucking his head next to hers.

Ember was almost in tears herself. As long as she had known Danny, he had been so strong, he had defeated the Ghost King almost single-handedly, he had fought off his older, evil side, and he had saved the worlds countless times. But now here he was, shaking from the pain he felt. She knew it on some level now, that through everything life was going to put them through, that no matter what pain they would endure, that nothing that was waiting for them tomorrow, could ever tear her from his side. And together, in the dark of Amity Park, they wept quietly together.


	5. Chapter 5 - Mission One

Decided that it was about time that I put out another chapter. So here it is!

Chapter 5 - Mission One

Danny wasn't sure what he was expecting when he thought about the GiW labs. But for some reason, the thought that the structure would look more like a large hospital, rather than some sort of underground bunker, never crossed his mind. He and Valerie were wearing white lab coats that covered the black half armor that they were wearing they also had card keys pinned to their immaculate white jackets that depicted them as Drs. Kent and Reese. Now came the tricky part. The overshadowing. The four in the group held their partner's hands as they watched them turn intangible and enter their bodies. Valerie shuddered and nearly fell as her instinct to try to rip out Dani was suppressed. Regardless, a head of sweat ran down her forehead as her eyes took on a green glow. Danny, who was far more experienced with overshadowing, didn't feel the regular nausea and immediate panic that one felt being overshadowed. He instead focused on the new consciousness filling out inside of his mind.

He could instantly recognize Ember. It was the same feeling as being in her presence, just far more intimate. Everything he thought was open to her mind as well. And vice versa. It was disorienting at first, but he focused and was able to take control of his body again. He felt different somehow. Like his ghost powers were more in tune now. More active in the back of his mind. He channeled some of his energy into making a clone. Instantly, one appeared beside him. He noticed some differences though. He now looked slightly bluer than before, and he was standing slightly differently. Almost like Ember. Then he spoke, "Alright, lets do this." Valerie and he picked up their bags, and walked briskly toward the building.

Although at a distance the massive building had appeared like a hospital of sorts, on closer inspection, he could see that the entire building was made out of stone, and the entire perimeter was blocked by an anti-ghost shield. If that wasn't enough, there was a platoon of armed guards on each flank of the building. That made over 100 guards at even intervals surrounding the building. There was a concrete tunnel that began just outside the ghost shield that ran through the glowing green wall, and into the main building. Once inside, where there was much lighter anti-ghost security, he was expected to Morph and search for the evidence.

Danny and Valerie made their way toward the tunnel. There were two cameras that followed their motions, watching them with an insensitive lens. It watched them as Danny swiped his key card, opening the door. Inside, the tunnel was extremely white, surgically so. The walls were immaculate, there was no sign of dust or dirt anywhere. They took a few tentative steps forward, and realized that they had in fact, made it inside.

The entrance hall that they now stood in was massive, with vaulting ceilings, and an air of superiority and grandness that was palpable. There were several scientists moving about, scurrying from one wing to another, never making eye contact, their heads low. These people were afraid of something. But despite the tense air, there was nothing that seemed to be an obvious cause for the anxiety. There were not nearly the number of guards that the group of four were expecting. It was as if the air itself carried some kind of malevolence.

Then a buzzing in Danny's ear made him pause, and he reached up one hand to answer the incoming call. "_Daniel, can you hear me?" _Valerie stopped, noticing his hesitation.

Danny responded, "Yes, I'm here. Is something wrong?"

"No. Frankly I would like to keep it that way." Said Vlad from over the communicator, "You will want to be taking the first right up ahead, that route should take you towards the wing that we are interested in. Remember, the main objective is reconnaissance. DO NOT LET YOURSELF GET CAUGHT!"

"Thanks for the directions," said Danny, getting stressed, "We've got it from here."

"Alright, but keep me posted."

The "pair" followed the curved wall until it branched off into a large hallway. This wing seemed to be specifically made for medical purposes. There were several men and women who were wearing long white lab coats with security badges hanging from their shirt. On either side of the hallway, Danny could see that many of these rooms housed patients, who were wired to sleek looking machines that were whirring quietly while they performed whatever it was that those machines do.

Danny was no doctor by any means, but he was able to recognize some things. Who knew that her sister's obsession with House would actually pay off? He knew that the rolling cabinets were called "crash carts." These were waist high boxes with several drawers that contained several instruments and medications that were designed to save someone who was on the brink of death, or having some kind of episode. And that was to be expected Danny realized, but he still wondered why there was an individual cart at _every door._ The thought that something was happening in this freakshow of a hospital that could cause so many "episodes" unnerved him on a certain level. Luckily though, they soon found one patient that was not being fretted over by one of the doctors. Slipping inside, they shut the door behind them, and slid the blinds closed.

Now Danny and Valerie were alone with the patient. It was a young man, barely in his twenties, who was wearing a distinctive military hairstyle and looked like he would be a fearsome opponent in direct combat. Danny was suddenly very thankful for the fact that this man was asleep, otherwise what they were planning to do would be much more difficult.

First, Valerie pulled a syringe from the nearby crash cart and almost tripped. "Sorry," said Valerie, but instead Dani's voice had come out of the woman's mouth. Danny was tempted to say something when he noticed that her eyes were green. Dani was in fact, in control now. Because of the influence, her hands moved deftly, mixing a number of drugs together in a small vial before drawing a fifth of the contents out and into the needle. "What is that," asked Danny interestedly.

"It's twenty margaritas in one shot." This stuff will knock him out and keep him from remembering anything when we are done collecting the blood sample. Danny just shrugged. He knew that Dani knew medicine fairly well by now and had no doubt that her concoction would work. Dani pointed up the syringe, tapped it a few times to make sure that there were no air bubbles, and then injected the clear fluid into the man's IV line. He convulsed, and then fell stone still as the drug took hold of his already unconscious mind.

Then Dani was free to take the two vials of blood that would be necessary and placed them into her bag. She now had four empty vials left. "Alright, we should try to get out of here now."

"I agree, let's split," said Dani, no need to stay here too long." But that's when a voice came over the intercom and everyone stopped. _ All employees please gather at the assembly hall for an important announcement. Again, all employees please report to the assembly hall. _And just as silently, each one of the scientists stopped anything that they were doing and flowed smoothly from their workstations presumably to the assembly hall. Danny and Valerie followed suit, blending into the crowd and following the people.

Almost five minutes later, through a number of white stone stairwells and hallways, Danny and Valerie entered a massive auditorium that seated easily a thousand people, and the stadium was rapidly filling. But despite the cavernous space, the room was almost silent. The only noise came from the sound of shoes on the floor. There wasn't even an occasional mutter of "sorry" when people bumped into each other. After finding seats that were on the edge of an aisle, just in case they needed a quick escape route, and they had a decent view of the auditorium. Almost a story below them sat the stage. It was a large white semicircle that had absolutely nothing in the way of furniture to boast of. It was even lacking a podium. There were harsh halogens that made the stage difficult to look at directly. In all, it had the exact same cold feel to it as did the rest of the entire structure that was now stories above them.

A lone man walked out and onto the stage, and suddenly every person had their eyes on him. He was a tall and thin man dressed almost entirely in black. His suit jacket to his tie and slacks, his entire ensemble was a black charcoal color. Even his eyes were dark pools that sent shivers down your spine when looking directly at them. He spoke in a rich and deep tone, almost mesmerizing in a sense. "As most of you already know, I am Sebastian Drake and I have been keeping a close eye on you for the past few weeks on out little research project. And I have some very good news for you. Our project is nearing its completion and soon our work will be done. The utopian world that we have all envisioned, a world without disease, a world without death, is nearing its fruition. Our dream of ghost hybridization is nearly complete. Soon we will have mastery of the ability to bond ghost energy to a human, and make humans, in all practical senses, immortal. It has been through our combined efforts that we have come so far, and we are ready to begin our first _human bonding sequence. _ This is a radical step forward for us. For years we have understood that humans could acquire a ghost body pre-mortem by being overexposed to ghost energy. This has occurred in two cases to date, and through our experiments, we have temporarily given these powers to others. But the thing that only _we _dreamed, was for a world where ghosts could reacquire a _human form. _ That's right. We are going to be making ghosts human again. And joining us today are our subjects _Tucker Foley and Samantha Manson._"

**A/N : MWAHAHAHAHA! Sam and Tucker are BACK! So what did you think? I was hoping to impress with a turnaround like that. In unrelated news, I've only gotten like two reviews so come on guys pick it up. And also, I wanted to thank the one guest who gave me an awesome review. Thank you so much sir! (I'm assuming here…) So as always, thanks for reading up until this point, and I hope to have another chapter up by next Sunday.**


	6. Chapter 6 - The Birth of a Phantom

**Hello and welcome back to THE PHANTOM THEORY (DUN DUN DUUUUNNNNNNNN)! I would like to thank you all for sticking with me on this story to chapter 6! Together we have reached 500+ views! Thanks for being awesome readers! Fixed Chapter 4, so now it is what Chapter 4 should have been, which is Chapter 4 and not Chapter 1, and oh, just go read it. On the agenda, I have been reading more fanfics from the people who write the 100k+ stories, and I am trying to pick up on some things. What I'm noticing is that in the longer stories, the pace is a lot slower and the authors allow for more character development. So I'm asking you to put whether or not you would appreciate something like that in the reviews, so whether or not you would like to see 5000+ words chapters instead of 1000+. And I want to point out that it would mean a lot more dialogue and less fighting by comparison (when we start getting into it). I would really appreciate it! So thank you and enjoy! **

Oh and p.s. … _Italics _are for voices in people's heads, like Ember is in Danny's head (at the moment) _**Bold Italics **_means shouting in one's head, which can cause migraines.

Chapter 6 – The Birth of a Phantom

Danny was speechless. After all the pain he went through, all he wanted was to be reunited with his friends. But something held him down, kept him from even moving. It was Ember, using her influence to keep him from moving a muscle. It probably saved his life. Ember made Danny aware of more than just his friends, and he now noticed that Sebastian had a certain look about him. Though his face was calm, his muscles had tensed, and his eyes were darting, looking for something. _Looking for __**us! **_

After a few moments of Sebastian's searching, he seemed to be satisfied and went back to his monologue. "Humans can contract a small amount of Ghost energy and then temporarily harness that energy. However, ghosts are different from humans in that a ghost can absorb this energy naturally. With a steady supply of this energy, they are able to achieve a state of immortality. It is the same power that powers their various powers. Therefore, if a human could absorb this power like a ghost, then they would be immortal in their ghost form. The human form however, which is the primary focus here, would become malnourished and die. What we found during our research is that the DNA in a Phantom has been changed by the ghost energy. This change allows ghost energy to be a byproduct of regular metabolism, keeping the ghost half alive. So in exchange for longevity and strength, the human form supplies the ghost with the energy to survive. Now we have a new issue, how can we give ghosts back their humanity? Simple. We have to splice in human DNA into the ghosts. So without further ado…"

Two scientists, wearing hazmat suits, approached Sam and Tucker, and rolling behind each of them were the same crash carts as before, the only difference being that all of the instruments were glowing a faint green, an obvious sign that the tools had been treated to affect ghosts. The two scientists deftly started IVs on the two teens and hooked them up to rebreathers. Then they drew long syringes filled with a fluid that was like mercury. Sebastian spoke again. "There exists in the ghost zone a specific virus. This 'Life Virus' affects ghosts on a genetic level, causing their body to begin producing human cells again. Then the ghost energy is absorbed through the ghost half and ensures that a human-ghost hybrid is achieved. On three gentlemen. One. Two. Three."

Danny could only watch, horrified, as the needles were plunged into Sam and Tucker's necks. Their bodies convulsed sickly against the restraints. So violently in fact, that even Sebastian took a step back. But after a few moments, the glow around the two teens faded and they developed a pallor. Their bodies relaxed, and they now looked as though they were asleep. But they were not quite human yet. They still had almost no color to their skin. Even Tucker was more of a pale green.

Danny had had enough. He Morphed and forced his body to move, against Ember's control. And rocketed forwards, punching Sebastian square in the jaw, sending him flying. Then he turned to his friends and started to pull out IVs and tried to get them out of the beds. "I wouldn't do that if I were you," said Sebastian, who had risen to his feet, blood running down the side of his cheek.

Danny ignored him and got back to his work, almost freeing Tucker. "I meant STOP! You will kill your friend like that. Without our life support, your friend will run out of nutrients in his blood to continue growing new cells, and he will die. The same goes for Miss Manson."

"What do you want?!" shouted Danny. "I've never done anything to you! Just let my friends go!"

"You see Phantom, that our virus is not perfect. We require something more." Sebastian drew and took aim with an odd looking pistol and shot it at Danny. It turned out to be similar to a taser gun, but was equipped with two needles instead of the metal prongs. Before Danny could react, Sebastian had fired, sending both into Danny's chest. He ripped them out as quickly as he could, but the damage had been done. He couldn't feel pain at the injuries, only a cold sensation. "I need a way to stop the virus from killing the human ghost hybrids when the process of creating a ghost is complete. Already, you must be feeling tired Danny…" Valerie's arms wrapped themselves around Danny, and with Dani's power, was able to fly the two of them out of the base.

"Follow them you idiots!" shouted Drake, and a pair of ghosts hidden in the crowd flew after the fleeting figures.

**A/N: And that is Chapter 6. I know its short guys and I'm sorry. Im just finding it hard to balance with homework, but I promised that I would have something for you today. I plan on revising it and making it better, but please accept my meager offering. Any thoughts, questions, please leave them in the reviews! I would love to hear from you guys :D Finally, I changed the rating to T because frankly, this story hasn't earned an M rating yet. If anything obscene happens, I will put it in an accompany story, and tone it down a bit. Please leave a review :D Until next week!**


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